diff nucleotide_diversity_pi.xml @ 22:95a05c1ef5d5

update to devshed revision aaece207bd01

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nucleotide_diversity_pi.xml	Mon Mar 11 11:28:06 2013 -0400
@@ -0,0 +1,34 @@
+<tool id="gd_nucleotide_diversity_pi" name="Nucleotide Diversity" version="1.0.0">
+  <description>: &amp;pi; and &amp;theta;</description>
+
+  <command interpreter="python">
+    nucleotide_diversity_pi.py "$saps" "$snps" "$intervals" "$indivs" "$output"
+    #for $individual_name, $individual_col in zip($snps.dataset.metadata.individual_names, $snps.dataset.metadata.individual_columns)
+      #set $arg = '%s:%s' % ($individual_col, $individual_name)
+      "$arg"
+    #end for
+  </command>
+
+  <inputs>
+    <param name="saps" type="data" format="gd_sap" label="SAP Dataset" />
+    <param name="snps" type="data" format="gd_snp" label="SNP Dataset" />
+    <param name="intervals" type="data" format="gd_covered_cds" label="Covered intervals" />
+    <param name="indivs" type="data" format="gd_indivs" label="Population individuals" />
+  </inputs>
+
+  <outputs>
+    <data name="output" format="txt" />
+  </outputs>
+
+  <help>
+**What it does**
+
+This tool computes values that estimate some basic parameters.
+
+**Output**
+
+the number of nonsyn SNPs, total number of nonsynon sites, piNon,
+the number of synon SNPs, total number of synon sites, piSyn, plus
+total length of covered intervals, thetaNon, thetaSyn
+  </help>
+</tool>